RNA Structures as Mediators of Neurological Diseases and as Drug Targets

Abstract

RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.

Genome-Wide Analysis of RNA Secondary Structure

“…As these modifications are covalent changes, they are stable; thus, in vitro studies can accurately report on their location. m 6 A, which does not modify the WC face, was initially identified using antibody-based techniques (23) to pull down regions of RNA with modifications, whereas ψ was identified by a chemical reaction with CMC (N-cyclohexyl-N9-(2-morpholinoethyl)-carbodiimide metho-p-toluenesulfonate), which modifies the ψ and provides reverse-transcription stops (14,93). m 1 A has been identified in toto in mRNA by liquid chromatography-tandem mass spectrometry, whereas antibody-based pulldowns coupled with next-generation sequencing have been used to map m 1 A-containing sequences genome-wide (24,59).…”

“…Parallel transcriptome-wide analysis of m 6 A covalent modifications by m 6 A immunoprecipitation with anti-m 6 A antibody and of hnRNPC binding sites by PAR-CLIP revealed overrepresentation of m 6 A sites in RNA regions associated with hnRNPC-binding targets (63). On the basis of biochemical studies with specific hnRNPC targets, the authors (63) proposed that m 6 A in the complementary strands of U-rich hairpins promotes hnRNPC binding by weakening the hairpin secondary structure.…”

“…Parallel transcriptome-wide analysis of m 6 A covalent modifications by m 6 A immunoprecipitation with anti-m 6 A antibody and of hnRNPC binding sites by PAR-CLIP revealed overrepresentation of m 6 A sites in RNA regions associated with hnRNPC-binding targets (63). On the basis of biochemical studies with specific hnRNPC targets, the authors (63) proposed that m 6 A in the complementary strands of U-rich hairpins promotes hnRNPC binding by weakening the hairpin secondary structure. Support for m 6 A regulation of RNA structure and hnRNPC binding as a genome-wide mechanism was provided by the observation that knockdown of two m 6 A methyltransferases reduced hnRNPC binding at more than 2,500 sites and also affected alternative splicing, promoting intron exclusion as deduced from the reduced presence of intron-exon junctions in RNA-Seq data (63).…”

“…In recent years, modifications of mRNAs, resulting in the so-called epitranscriptome, have become increasingly recognized as important regulatory events. In particular, ψ and m 6 A modifications have apparent implications for RNA structural stability and half-life. With regard to structural stability, ψ can base pair noncanonically with all four nucleotides.…”

“…Whereas ψ is relatively rare in mRNAs, reported at only several hundred mRNA sites in studies on yeast and human cells (14,93), m 6 A is a common covalent modification of mRNAs, with many thousands of mRNA sites reported for mouse and human cell lines (23) as well as mouse (81) and human (23) brain tissue. m 6 A sites are conserved between mouse and human.…”